Pseudopeptidic Macrocycles Research Articles

Continuous Flow Processes as an Enabling Tool for the Synthesis of Constrained Pseudopeptidic Macrocycles.

Herein we report our efforts to develop a continuous flow methodology for the efficient preparation of pseudopeptidic macrocyclic compounds containing the hexahydropyrrolo-[3,4-f]-isoindolocyclophane scaffold and involving four coupled substitution reactions in the macrocyclization process. Appropriate design of a supported base permitted the continuous production of the macrocycles even at large scales, taking advantage of the positive template effect promoted by the bromide anions. In addition, the use of flow protocols allowed a ca. 20-fold increase in productivity as well as reducing the environmental impact almost 2 orders of magnitude, in comparison with the related batch macrocyclization process.

Immobilized Supramolecular Systems as Efficient Synzymes for CO2 Activation and Conversion

AbstractSupramolecular catalysis can provide distinct advantages for the catalytic conversion of CO2 into carbonates by cycloaddition to epoxides. For example, the absence of metals in the catalytic site, and the easy design for optimization. The incorporation of multiple functionalities in pseudopeptidic macrocycles with a pendant arm allows catalytic systems to be obtained where halide anions (nucleophilic activating agents for epoxides), hydrogen bond acceptor sites (activating agents for epoxides and stabilizing sites for anionic intermediates), and amine groups (Lewis basic sites for activating CO2) are in proximity. This allows a high activity in the cycloaddition of CO2 to styrene oxide under mild conditions (turnover number (TON) = 900, CO2 balloon, 100 °C, 5 h). The primary amino groups in the arm facilitate the immobilization of these macrocyclic structures in cross‐linked polymeric matrices containing ammonium halide fragments. Such multifunctional insoluble polymers afford excellent catalytic results with high TON and turnover frequency values and remarkable productivities (>10 gprod gresin−1 h−1). This activity is maintained for a variety of epoxides and is retained after several catalytic runs. Their performance is significantly higher than those reported for most heterogenous supramolecular catalytic systems for CO2 transformation into carbonates.

Pseudopeptidic macrocycles as cooperative minimalistic synzyme systems for the remarkable activation and conversion of CO2 in the presence of the chloride anion

A series of pseudopeptidic compounds have been assayed as organocatalyts for the conversion of CO2 into organic carbonates through a cooperative multifunctional mechanism.

Unraveling the Multistimuli Responses of a Complex Dynamic System of Pseudopeptidic Macrocycles

Dynamic combinatorial libraries (DCLs) are excellent benchmark models to study the stimuli-responsiveness of chemical networks. However, increasingly complex systems are difficult to analyze with simple data analysis methods, because many variables and connections must be considered for their full understanding. Here we propose the use of multivariate data analysis methods to bisect the evolution of a complex synthetic dynamic library of pseudopeptidic macrocycles, containing side chains with charges of different sign. Several stimuli (ionic strength, pH and the presence of a biogenic polyamine) were applied to the same dynamic chemical mixture, and the adaptation of the whole system was characterized by HPLC and analyzed with principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods. Both multivariate data analysis chemometric approaches are an excellent combination to extract both qualitative and semi-quantitative information about the adaptive process of the library upon the action of each stimulus. The resolution of the system with these chemometric tools proved to be especially useful when two inter-connected stimuli were combined in the same dynamic system. Our results demonstrate the utility of these two approaches for the analysis of complex dynamic chemical systems and open the way toward the application of these powerful tools in the emergent field of systems chemistry.

Oxoanion binding to a cyclic pseudopeptide containing 1,4-disubstituted 1,2,3-triazole moieties.

A macrocyclic pseudopeptide 3 is described featuring three amide groups and three 1,4-disubstituted 1,2,3-triazole units along the ring. This pseudopeptide was designed such that the amide NH groups and the triazole CH groups converge toward the cavity, thus creating an environment well suited for anion recognition. Conformational studies in solution combined with X-ray crystallography confirmed this preorganisation. Solubility of 3 restricted binding studies to organic media such as 5 vol% DMSO/acetone or DMSO/water mixtures with a water content up to 5 vol%. These binding studies demonstrated that 3 binds to a variety of inorganic anions in DMSO/acetone including chloride, nitrate, sulfate, and dihydrogenphosphate anions. In the more competitive DMSO/water mixtures, only affinity to the more strongly coordinating oxoanions is retained. Quantitative binding studies showed that dihydrogen phosphate complexation in DMSO/water involves the dimer of the H2PO4- anion. By contrast, sulfate and hydrogenpyrophosphate complexation involves a stepwise process comprising formation of a 1 : 1 complex followed by a 2R : 1A complex in which two molecules of 3 (R) bind to a single anion (A). While the second binding equilibrium is associated with a much smaller stability constant in comparison with the first one in the case of sulfate complexation, the two binding constants are of similar magnitude in the case of the hydrogenpyrophosphate anion. Formation of the 2R : 1A complex was attributed to the fact that the cavity size and rigidity of 3 prevents saturation of all hydrogen acceptor sites on the anionic guests.

Entropy-driven homochiral self-sorting of a dynamic library.

A dynamic mixture of stereoisomeric macrocycles derived from glutamic acid displayed a homochiral self-selection when increasing the acetonitrile content of the aqueous mixed medium. The homochiral self-sorting required the anionic form of the side chains and increased at higher temperature, implying an entropic origin. Conformational analysis (NMR and MD simulations) allowed us to explain the observed behaviour. The results show that entropy can play a role in the homochiral self-sorting in adaptive bio-inspired chemical systems.

Salt-induced adaptation of a dynamic combinatorial library of pseudopeptidic macrocycles: unraveling the electrostatic effects in mixed aqueous media.

Dynamic combinatorial libraries are powerful systems for studying adaptive behaviors and relationships, as models of more complex molecular networks. With this aim, we set up a chemically diverse dynamic library of pseudopeptidic macrocycles containing amino-acid side chains with differently charged residues (negative, positive, and neutral). The responsive ability of this complex library upon the increase of the ionic strength has been thoroughly studied. The families of the macrocyclic members concentrating charges of the same sign showed a large increase in its proportion as the ionic strength increases, whereas those with residues of opposite charges showed the reverse behavior. This observation suggested an electrostatic shielding effect of the salt within the library of macrocycles. The top-down deconvolution of the library allowed us to obtain the fundamental thermodynamic information connecting the library members (exchange equilibrium constants), as well as to parameterize the adaptation to the external stimulus. We also visualized the physicochemical driving forces for the process by structural analysis using NMR spectroscopy and molecular modeling. This knowledge permitted the full understanding of the whole dynamic library and also the de novo design of dynamic chemical systems with tailored co-adaptive relationships, containing competing or cooperating species. This study highlights the utility of dynamic combinatorial libraries in the emerging field of systems chemistry.

The Role of the Amino Acid-Derived Side Chain in the Preorganization of C2-Symmetric Pseudopeptides: Effect on SN2 Macrocyclization Reactions

A family of pseudopeptidic macrocycles containing non-natural amino acids have been synthesized. The macrocyclization reaction has been studied experimentally and computationally, demonstrating the key role of both the amino acid side chain and the catalytic bromide anion. The bromide anion acts as an external template assisting the folding of the open-chain precursor in a proper conformation. Computations revealed that in the presence of the anion, the effect of the side chain on the energy barrier for the macrocyclization is very small. However, the effect on the conformational equilibria of the open-chain precursors is very important. Overall, the stabilization of those conformation(s) in which the two reactive ends of the open-chain intermediate are located at short distances from each other with the correct orientation is the critical parameter defining the success of the macrocyclization. The best yield was found for the compound containing cyclohexylalanine, for which the computationally-predicted most stable conformer in the presence of Br(-) has a proper preorganization for cyclization. The remarkable agreement obtained between experiments and theory reveals that the computational approach here considered can be of great utility for the prediction of the behavior of other related systems and for the design of appropriate synthetic routes to new macrocyclic compounds.

The emergence of halophilic evolutionary patterns from a dynamic combinatorial library of macrocyclic pseudopeptides

The increase of the ionic strength amplifies the species bearing acidic side chains from a bio-inspired dynamic combinatorial library of macrocyclic pseudopeptides, in close resemblance to the evolution observed for the proteins of halophilic microorganisms.

Template Effects in SN2 Displacements for the Preparation of Pseudopeptidic Macrocycles

Macrocyclisation reactions of C(2)-symmetric pseudopeptides containing central pyridine-derived spacers are affected by the presence of different anions. The selection of the proper anion gives excellent results for the preparation of the corresponding macrocyclic structures. Kinetic studies show that the presence of those anions enhances both the yield and the rate of the reaction. Computational studies at the B3LYP/6-31G* level have allowed us to rationalise the experimental results. The obtained transition states (TSs) show that the interaction between the anion and the open-chain pseudopeptidic chain has a stabilising effect. The anion stabilises the two TSs involved: the first one, which involves the formation of the initial bond between the two subunits and leads to an open-chain intermediate, and the second one, which precedes the formation of the cyclic structure. The optimum anion (Br(-) when the central spacer is derived from 2,6-bis(aminomethyl)pyridine, is able to act as a template, in that it forces the two ends of the open-chain intermediate to approach each other by forming hydrogen bonds with the two amino acid subunits present in the intermediate. This stabilises the second TS to a greater extent than the first one, and thus, favours macrocyclisation over the competing oligomerisation reactions. The computational calculations also allowed us to predict the outcome of new experiments. Accordingly, the synthesis of the pseudopeptidic macrocycle derived from 2,6-diaminopyridine was not successful under the optimised conditions previously used. Nevertheless, calculations predicted that in this case Cl(-) should be more efficient than Br(-), and this was subsequently experimentally confirmed. Interestingly, the presence of different substituents on the constituent amino acids seems to play a minor role in the overall process.

ChemInform Abstract: Cyclic Peptidomimetics and Pseudopeptides from Multicomponent Reactions

AbstractReview: 107 refs.

Structurally disfavoured pseudopeptidic macrocycles through anion templation

An anionic dicarboxylate is able to template the formation of geometrically disfavoured macrocycles from a dynamic covalent mixture of open chain oligoimines.

Synthesis and Evaluation of Pseudopeptidic Fluorescence pH Probes for Acidic Cellular Organelles: In Vivo Monitoring of Bacterial Phagocytosis by Multiparametric Flow Cytometry

AbstractA new family of fluorescent anthracenic pH probes has been synthesized, chemically characterized, and their photophysical properties have been investigated by steady‐state and time‐resolved fluorescence spectroscopy. The ability of these compounds to monitor pH has been investigated in solution and it was found that molecules 1–12 can act as fluorescent sensors for pH in a range between 4.6 and 6.5. This range corresponds to the pH of acidic organelles in the cell (pH 4.5–6.0) for which a limited number of probes are described. The acid–base behavior of each sensor varies slightly depending on the nature of substituents close to the amines present in the molecules. Thus, the pKa of this family of compounds can be finely tuned by the appropriate selection of the synthetic building blocks at the design stage. To test the potential diagnostic applications of this family of probes, macrocyclic pseudopeptide 2 was used to monitor the phagocytosis of a culture of GFP‐labelled bacteria by human monocytic cells U937 using flow cytometry as the analytical tool. It was found that the occurrence of bacterial killing was concomitant with the production of reactive oxygen species and a drop in pH, the latter monitored indirectly by macrocyclic sensor 2, which suggests its potential use for diagnostic purposes.

Structural Diversity in the Self‐Assembly of Pseudopeptidic Macrocycles

The self-assembling abilities of several pseudopeptidic macrocycles have been thoroughly studied both in the solid (SEM, TEM, FTIR) and in solution (NMR, UV, CD, FTIR) states. Detailed microscopy revealed large differences in the morphology of the self-assembling micro/nanostructures depending on the macrocyclic chemical structures. Self-assembly was triggered by the presence of additional methylene groups or by changing from para to meta geometry of the aromatic phenylene backbone moiety. More interestingly, the nature of the side chain also plays a fundamental role in some of the obtained nanostructures, thus producing structures from long fibers to hollow spheres. These nanostructures were obtained in different solvents and on different surfaces, thus implying that the chemical information for the self-assembly is contained in the molecular structure. Dilution NMR studies (chemical shift and self-diffusion rates) suggest the formation of incipient aggregates in solution by a combination of hydrogen-bonding and pi-pi interactions, thus implicating amide and aryl groups, respectively. Electronic spectroscopy further supports the pi-pi interactions because the compounds that lead to fibers show large hypochromic shifts in the UV spectra. Moreover, the fiber-forming macrocycles also showed a more intense CD signature. The hydrogen-bonding interactions within the nanostructures were also characterized by attenuated total-reflectance FTIR spectroscopy, which allowed us to monitor the complete transition from the solution to the dried nanostructure. Overall, we concluded that the self-assembly of this family of pseudopeptidic macrocycles is dictated by a synergic action of hydrogen-bonding and pi-pi interactions. The feasibility and geometrical disposition of these interactions finally render a hierarchical organization, which has been rationalized with a proposal of a model. The understanding of the process at the molecular level has allowed us to prepare hybrid soft materials.

Molecular recognition of N-protected dipeptides by pseudopeptidic macrocycles: a comparative study of the supramolecular complexes by ESI-MS and NMR

The molecular recognition properties of pseudopeptidic macrocycles have been studied by ESI-MS and NMR spectroscopy, as highly complementary experimental techniques in solution and in the gas phase. We used ESI-MS competition experiments for the high throughput screening of the supramolecular interaction between four macrocyclic receptors and different peptide-like substrates in solution, rendering the best-fitted host-guest pairs. Further insights on the non-covalent recognition process in the gas-phase were obtained through collision induced dissociation (CID) experiments. Solution studies using NMR spectroscopy ((1)H NMR titrations, NOESY and DOSY) were carried out to prove the validity of ESI-MS as a high-throughput screening method for studying the molecular recognition of the investigated pseudopeptidic macrocycles. A clear selectivity for N-protected dipeptides over N-protected amino acids, and a slight preference for dipeptides bearing aromatic side chains were observed. On the basis of the results obtained from this approach, a mode of binding has been proposed.

Thieme Chemistry Journal Awardees - Where Are They Now? Macrocyclic Peptide Chemistry Inspired by Nature - From Chiral Artificial Receptors toward Molecular Devices

This account surveys our efforts in the design, syntheses and fundamental applications of oxazole- and imidazole-containing macrocyclic pseudopeptide platforms related to Lissoclinum alkaloids.

Crystal structures of the HCl salts of pseudopeptidic macrocycles display “knobs into holes” hydrophobic interactions between aliphatic side chains

The crystal structures of three HCl salts of pseudopeptidic macrocycles show a H-bonding tubular stack of the rings, where the amino acidic side chains (Val, Leu, Ile) display an inter-columnar “knobs into holes” hydrophobic interaction pattern.

Use of Fluorescence Spectroscopy To Study Polymeric Materials with Porous Structure Based on Imprinting by Self-Assembled Fibrillar Networks

Different polymeric materials have been prepared from the organogels formed by a polymerizable methacrylic mixture (methyl methacrylate/ethylene glycol dimethacrylate, 1:1, w/w) and the macrocyclic pseudopeptide 1. The use of (2,4,6-trimethylbenzoyl)diphenylphosphine oxide as a very efficient radical initiator allows polymeric materials in which the structure of the fibrils formed by self-assembly of the organogelator 1 is truly preserved to be obtained. Removal of the pseudopeptidic molecule provides materials with a porous structure reflecting that of the original self-assembled fibrils. The use of fluorescent probes such as rhodamine B and pyrene greatly facilitate the study of the porous structures formed and, accordingly, that of the morphology of the original fibrils. Those studies reveal the presence of a permanent porosity and the organization of the substructures as a porous network. This confirms the existence of a nucleation and growth mechanism for the generation of the fibrils, giving rise to the formation of spherulitic structures. Those spherulites are additionally linked by connections of variable size. A series of diffusion experiments allowed establishment of a direct dependence of the inner porosity of the materials on the amount of self-organizing template used for their preparation.

Designed Folding of Pseudopeptides: The Transformation of a Configurationally Driven Preorganization into a Stereoselective Multicomponent Macrocyclization Reaction

The efficient synthesis of large-ring pseudopeptidic macrocycles through a multicomponent [2+2] reductive amination reaction is described. The reaction was entirely governed by the structural information contained in the corresponding open-chain pseudopeptidic bis(amidoamine) precursors, which have a rigid (R,R)-cyclohexane-1,2-diamine moiety. A remarkable match/mismatch relationship between the configurations of the chiral centers of the cyclic diamine and those of the peptidic frame was observed. The macrocyclic tetraimine intermediates have been studied in detail by NMR spectroscopy, circular dichroism (CD), and molecular modeling, and the results support the appropriate preorganization induced by the match combination of the chiral centers. We have also synthesized the corresponding open-chain bis(imine) model compounds. The structural studies (NMR spectroscopy, CD, modeling) of these systems showed an intrinsically lower reactivity of the mismatch combination, even when the product of the reaction was acyclic. In addition, a synergistic effect between the two chiral substructures for the correct folding of the molecules was observed. Finally, X-ray analysis of the HCl salt of one of the macrocycles showed an interesting pattern; the macrocyclic rings stack in columnar aggregates leaving large interstitial channels filled with water-solvated chloride anions.

Supramolecular Control for the Modular Synthesis of Pseudopeptidic Macrocycles through an Anion-Templated Reaction

The anion-templated synthesis of different pseudopeptidic macrocycles has been studied in detail by using a multidisciplinary approach. The reaction between an open-chain pseudopeptidic diamine and the appropriate dialdehyde is highly affected by the presence of the best fitting anionic template. The formation of the corresponding macrocyclic tetraimino-template supramolecular complex is demonstrated by NMR (ROESY and PGSE) and mass spectrometry (ESI-TOF). These supramolecular complexes can be easily reduced to the corresponding more stable tetraamine macrocycles. Accordingly, we have used this reaction to efficiently synthesize a family of new pseudopeptidic macrocycles in a one-pot two-steps anion-templated reductive amination reaction, which comprises a multicomponent macrocyclization through the selective formation of four chemical bonds to yield a unique macrocyclic structure. Different variables like the aliphatic spacer between amino acidic moieties, geometry of the dialdehyde, and structure of the amino acid side chains were thoroughly studied, and their effect in the formation and stability of the supramolecular complexes discussed. The conformational preorganization induced by the template has been monitored by circular dichroism, reflecting the differences observed in the isolated yields, as well as by NMR spectroscopy. This effect has been also supported by molecular modeling. All the experimental and theoretical techniques were strongly consistent and reflected the same trends by comparing the different structural variables introduced in the system.